Unarmed men marched through the streets waving sticks and chanting "No Raila, no peace" in support of opposition leader Raila Odinga who is behind Kenyatta by a margin of 1.4 million ballots. Violence has also been reported in the vicinity of the country's capital, Nairobi, and in various shantytowns surrounding the city, most notably Mathare.
Odinga had said hackers could have used the identity of a top election official, who was tortured and murdered days before the vote.
Nasa spokesman Musalia Mudavadi said that the coalition would submit its evidence of fraud to the election board - but appealed for Kenyans to remain "calm".
Many Kenyans are hoping the results of the already disputed vote will be announced within hours.
A police officer at the scene, who spoke on the condition of anonymity due to restrictions over speaking to the media, said two people were killed during the riots. Many businesses remain closed amid fears of violence.
Meanwhile, International election observers Thursday called for restraint as Kenyans await the announcement of the official results from the nationwide polls.
Businesses have been closed in the central business district since the vote.
Provisional results showed Kenyatta, whose father was Kenya's first president after independence from British colonial rule, holding a strong lead with votes from 98 per cent of polling stations counted.
The IGAD chairman and Ethiopian Prime Minister Hailemariam Desalegn urged Kenyans to respect the election results.
Kura Yangu Sauti Yangu, a set of rights groups coordinated by the Kenya Human Rights Commission, commented on the situation via a statement, saying that the voting had been orderly, but that early results were "completely unverifiable".
Opposition candidate Raila Odinga, whose rejection of the 2007 presidential election result triggered widespread bloodshed, has challenged the results released so far. Businesses have been closed in Nairobi's central business district since Tuesday's vote.
Chebukati said "hacking was attempted but did not succeed" and tallying of final results was continuing.
The commission's rebuttal came after an opposition official said he had information from "confidential sources" showing that Odinga had defeated incumbent candidate President Uhuru Kenyatta by just under 300,000 votes.
NAN reports that in 2007, tallying was stopped and the incumbent president declared the victor, triggering an outcry from Odinga's camp.